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From this sentence I read:

これらの手法はクリティカルセクションが(例えば100μ秒以内などの)一定時間以内に終わるよう精密にプログラミングすることを要求する。

How am I supposed to pronounce μ秒 ? Should I pronounce it as "mu byou"? or "micro byou"? I also looked up μm (micrometer) and found that it is マイクロメートル. I found a few other ones that are just loanwords like マイクロアンペア for μA. Can this convention be applied to 秒 as well?

Is there a convention to use with other measurements too? For example "pico", "nano", "femto"?

10

μ as a character (記号) would be pronounced ミュー. But when used as a measurement I would agree with @Teno's findings that it will be pronounced マイクロ, based off of the link he provided.

If you take a look at the Wikipedia page for 秒 you'll find that they write out マイクロ秒 on the page (though not in direct relation to μ秒), http://ja.wikipedia.org/wiki/秒.

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